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NMR processing:
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NMR assignment:
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Side-chains:
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NOEs:
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UNIO Candid
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Structure from NMR restraints:
Ab initio:
GeNMR
Cyana
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Fragment-based:
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Template-based:
GeNMR
I-TASSER
Refinement:
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Structure from chemical shifts:
Fragment-based:
WeNMR CS-Rosetta
BMRB CS-Rosetta
Homology-based:
CS23D
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Torsion angles from chemical shifts:
Preditor
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Secondary structure from chemical shifts:
CSI (via RCI server)
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MICS caps, β-turns
d2D
PECAN
Flexibility from chemical shifts:
RCI
Interactions from chemical shifts:
HADDOCK
Chemical shifts re-referencing:
Shiftcor
UNIO Shiftinspector
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NMR model quality:
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Chemical shifts:
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iCing
RDCs:
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Protein geomtery:
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iCing
PSVS
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SAVES2 or SAVES4
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Ramachandran Plot
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Verify_3D
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Quality Control Check
NMR spectrum prediction:
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V-NMR
Flexibility from structure:
Backbone S2
Methyl S2
B-factor
Molecular dynamics:
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Chemical shifts prediction:
From structure:
Shiftx2
Sparta+
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CH3shift- Methyl
ArShift- Aromatic
ShiftS
Proshift
PPM
CheShift-2- Cα
From sequence:
Shifty
Camcoil
Poulsen_rc_CS
Disordered proteins:
MAXOCC
Format conversion & validation:
CCPN
From NMR-STAR 3.1
Validate NMR-STAR 3.1
NMR sample preparation:
Protein disorder:
DisMeta
Protein solubility:
camLILA
ccSOL
Camfold
camGroEL
Zyggregator
Isotope labeling:
UPLABEL
Solid-state NMR:
sedNMR


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Old 02-22-2011, 10:40 PM
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Default Targeting Bacterial Membranes: Identification of Pseudomonas aeruginosa D-Arabinose-5P Isomerase and NMR Characterisation of its Substrate Recognition and Binding Properties.

Targeting Bacterial Membranes: Identification of Pseudomonas aeruginosa D-Arabinose-5P Isomerase and NMR Characterisation of its Substrate Recognition and Binding Properties.

Targeting Bacterial Membranes: Identification of Pseudomonas aeruginosa D-Arabinose-5P Isomerase and NMR Characterisation of its Substrate Recognition and Binding Properties.

Chembiochem. 2011 Feb 17;

Authors: Airoldi C, Sommaruga S, Merlo S, Sperandeo P, Cipolla L, Polissi A, Nicotra F

The identification and characterisation of Pseudomonas aeruginosa KdsD (Pa-KdsD), a D-arabinose-5P isomerase involved in the biosynthesis of 3-deoxy-D-manno-oct-2-ulosonic acid and thus of lipopolysaccharide (LPS), are reported. We have demonstrated that KdsD is essential for P. aeruginosa survival and thus represents a key target for the development of novel antibacterial drugs. The key amino acid residues for protein activity have been identified. The structural requirements for substrate recognition and binding have been characterised for the wild-type protein, and the effect of mutations of the key residues on catalytic activity and binding have been evaluated by saturation transfer difference (STD) NMR spectroscopy. Our data provide important structural information for the rational design of new KdsD inhibitors as potential antibacterial drugs.

PMID: 21337483 [PubMed - as supplied by publisher]



Source: PubMed
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